CONFLIST PTR        PTRBK PTR01 PTR-1 PTR-2

NATOM    PTRBK      6
NATOM    PTR01      20
NATOM    PTR-1      19
NATOM    PTR-2      18 

IATOM    PTRBK  N   0
IATOM    PTRBK  H   1
IATOM    PTRBK  CA  2
IATOM    PTRBK  HA  3
IATOM    PTRBK  C   4
IATOM    PTRBK  O   5
IATOM    PTR01  CB  0
IATOM    PTR01 1HB  1
IATOM    PTR01 2HB  2
IATOM    PTR01  CG  3
IATOM    PTR01  CD1 4
IATOM    PTR01  HD1 5
IATOM    PTR01  CD2 6
IATOM    PTR01  HD2 7
IATOM    PTR01  CE1 8
IATOM    PTR01  HE1 9
IATOM    PTR01  CE2 10
IATOM    PTR01  HE2 11
IATOM    PTR01  CZ  12
IATOM    PTR01  OH  13
IATOM    PTR01  P   14
IATOM    PTR01  O1P 15
IATOM    PTR01  O2P 16
IATOM    PTR01 HO2P 17
IATOM    PTR01  O3P 18
IATOM    PTR01 HO3P 19
IATOM    PTR-1  CB  0
IATOM    PTR-1 1HB  1
IATOM    PTR-1 2HB  2
IATOM    PTR-1  CG  3
IATOM    PTR-1  CD1 4
IATOM    PTR-1  HD1 5
IATOM    PTR-1  CD2 6
IATOM    PTR-1  HD2 7
IATOM    PTR-1  CE1 8
IATOM    PTR-1  HE1 9
IATOM    PTR-1  CE2 10
IATOM    PTR-1  HE2 11
IATOM    PTR-1  CZ  12
IATOM    PTR-1  OH  13
IATOM    PTR-1  P   14
IATOM    PTR-1  O1P 15
IATOM    PTR-1  O2P 16
IATOM    PTR-1 HO2P 17
IATOM    PTR-1  O3P 18
IATOM    PTR-2  CB  0
IATOM    PTR-2 1HB  1
IATOM    PTR-2 2HB  2
IATOM    PTR-2  CG  3
IATOM    PTR-2  CD1 4
IATOM    PTR-2  HD1 5
IATOM    PTR-2  CD2 6
IATOM    PTR-2  HD2 7
IATOM    PTR-2  CE1 8
IATOM    PTR-2  HE1 9
IATOM    PTR-2  CE2 10
IATOM    PTR-2  HE2 11
IATOM    PTR-2  CZ  12
IATOM    PTR-2  OH  13
IATOM    PTR-2  P   14
IATOM    PTR-2  O1P 15
IATOM    PTR-2  O2P 16
IATOM    PTR-2  O3P 17

ATOMNAME PTRBK    0  N
ATOMNAME PTRBK    1  H
ATOMNAME PTRBK    2  CA
ATOMNAME PTRBK    3  HA
ATOMNAME PTRBK    4  C
ATOMNAME PTRBK    5  O
ATOMNAME PTR01    0  CB
ATOMNAME PTR01    1 1HB
ATOMNAME PTR01    2 2HB
ATOMNAME PTR01    3  CG
ATOMNAME PTR01    4  CD1
ATOMNAME PTR01    5  HD1
ATOMNAME PTR01    6  CD2
ATOMNAME PTR01    7  HD2
ATOMNAME PTR01    8  CE1
ATOMNAME PTR01    9  HE1
ATOMNAME PTR01   10  CE2
ATOMNAME PTR01   11  HE2
ATOMNAME PTR01   12  CZ
ATOMNAME PTR01   13  OH
ATOMNAME PTR01   14  P
ATOMNAME PTR01   15  O1P
ATOMNAME PTR01   16  O2P
ATOMNAME PTR01   17 HO2P
ATOMNAME PTR01   18  O3P
ATOMNAME PTR01   19 HO3P
ATOMNAME PTR-1    0  CB
ATOMNAME PTR-1    1 1HB
ATOMNAME PTR-1    2 2HB
ATOMNAME PTR-1    3  CG
ATOMNAME PTR-1    4  CD1
ATOMNAME PTR-1    5  HD1
ATOMNAME PTR-1    6  CD2
ATOMNAME PTR-1    7  HD2
ATOMNAME PTR-1    8  CE1
ATOMNAME PTR-1    9  HE1
ATOMNAME PTR-1   10  CE2
ATOMNAME PTR-1   11  HE2
ATOMNAME PTR-1   12  CZ
ATOMNAME PTR-1   13  OH
ATOMNAME PTR-1   14  P
ATOMNAME PTR-1   15  O1P
ATOMNAME PTR-1   16  O2P
ATOMNAME PTR-1   17 HO2P
ATOMNAME PTR-1   18  O3P
ATOMNAME PTR-2    0  CB
ATOMNAME PTR-2    1 1HB
ATOMNAME PTR-2    2 2HB
ATOMNAME PTR-2    3  CG
ATOMNAME PTR-2    4  CD1
ATOMNAME PTR-2    5  HD1
ATOMNAME PTR-2    6  CD2
ATOMNAME PTR-2    7  HD2
ATOMNAME PTR-2    8  CE1
ATOMNAME PTR-2    9  HE1
ATOMNAME PTR-2   10  CE2
ATOMNAME PTR-2   11  HE2
ATOMNAME PTR-2   12  CZ
ATOMNAME PTR-2   13  OH
ATOMNAME PTR-2   14  P
ATOMNAME PTR-2   15  O1P
ATOMNAME PTR-2   16  O2P
ATOMNAME PTR-2   17  O3P

#1.Basic Conformer Information: name, pka, em, rxn.
#23456789A123456789B123456789C
PROTON   PTR01      0
PKA      PTR01      0.0
ELECTRON PTR01      0
EM       PTR01      0.0
RXN      PTR01      -9.95 

PROTON   PTR-1      -1
PKA      PTR-1      5.90
ELECTRON PTR-1      0
EM       PTR-1      0.0
RXN      PTR-1      -24.774 

PROTON   PTR-2      -2
PKA      PTR-2      9.28
ELECTRON PTR-2      0
EM       PTR-2      0
RXN      PTR-2      -69.433
tructure Connectivity
#23456789A123456789B123456789C123456789D123456789E123456789F123456789G123456789H123456789I
#23456789A123456789B123456789C123456789D123456789E123456789F123456789G123456789H123456789I
#ONNECT   conf atom  orbital  ires conn ires conn ires conn ires conn
#ONNECT |-----|----|---------|----|----|----|----|----|----|----|----|----|----|----|----|
CONNECT  PTRBK  N   sp2       -1    C   0     CA  0     H
CONNECT  PTRBK  H   s         0     N
CONNECT  PTRBK  CA  sp3       0     N   0     C   0     CB  0     HA
CONNECT  PTRBK  HA  s         0     CA
CONNECT  PTRBK  C   sp2       0     CA  0     O   1     N
CONNECT  PTRBK  O   sp2       0     C

CONNECT  PTR01  CB  sp3       0     CA  0     CG  0     1HB 0    2HB
CONNECT  PTR01 1HB  s         0     CB
CONNECT  PTR01 2HB  s         0     CB
CONNECT  PTR01  CG  sp2       0     CB  0     CD1 0     CD2
CONNECT  PTR01  CD1 sp2       0     CG  0     CE1 0     HD1
CONNECT  PTR01  HD1 s         0     CD1
CONNECT  PTR01  CD2 sp2       0     CG  0     CE2 0     HD2
CONNECT  PTR01  HD2 s         0     CD2
CONNECT  PTR01  CE1 sp2       0     CD1 0     CZ  0     HE1
CONNECT  PTR01  HE1 s         0     CE1
CONNECT  PTR01  CE2 sp2       0     CD2 0     CZ  0     HE2
CONNECT  PTR01  HE2 s         0     CE2
CONNECT  PTR01  CZ  sp2       0     CE1 0     CE2 0     OH
CONNECT  PTR01  OH  sp3       0     CZ  0     P
CONNECT  PTR01  P   sp3       0     OH  0     O1P 0     O2P 0    O3P     
CONNECT  PTR01  O1P sp2       0     P
CONNECT  PTR01  O2P sp3       0     P   0    HO2P
CONNECT  PTR01 HO2P s         0     O2P  
CONNECT  PTR01  O3P sp3       0     P   0    HO3P
CONNECT  PTR01 HO3P s         0     O3P

CONNECT  PTR-1  CB  sp3       0     CA  0     CG  0     1HB 0    2HB
CONNECT  PTR-1 1HB  s         0     CB
CONNECT  PTR-1 2HB  s         0     CB
CONNECT  PTR-1  CG  sp2       0     CB  0     CD1 0     CD2
CONNECT  PTR-1  CD1 sp2       0     CG  0     CE1 0     HD1
CONNECT  PTR-1  HD1 s         0     CD1
CONNECT  PTR-1  CD2 sp2       0     CG  0     CE2 0     HD2
CONNECT  PTR-1  HD2 s         0     CD2
CONNECT  PTR-1  CE1 sp2       0     CD1 0     CZ  0     HE1
CONNECT  PTR-1  HE1 s         0     CE1
CONNECT  PTR-1  CE2 sp2       0     CD2 0     CZ  0     HE2
CONNECT  PTR-1  HE2 s         0     CE2
CONNECT  PTR-1  CZ  sp2       0     CE1 0     CE2 0     OH
CONNECT  PTR-1  OH  sp3       0     CZ  0     P
CONNECT  PTR-1  P   sp3       0     OH  0     O1P 0     O2P 0    O3P
CONNECT  PTR-1  O1P sp2       0     P
CONNECT  PTR-1  O2P sp3       0     P   0    HO2P
CONNECT  PTR-1 HO2P s         0     O2P
CONNECT  PTR-1  O3P sp2       0     P   

CONNECT  PTR-2  CB  sp3       0     CA  0     CG  0     1HB 0    2HB
CONNECT  PTR-2 1HB  s         0     CB
CONNECT  PTR-2 2HB  s         0     CB
CONNECT  PTR-2  CG  sp2       0     CB  0     CD1 0     CD2
CONNECT  PTR-2  CD1 sp2       0     CG  0     CE1 0     HD1
CONNECT  PTR-2  HD1 s         0     CD1
CONNECT  PTR-2  CD2 sp2       0     CG  0     CE2 0     HD2
CONNECT  PTR-2  HD2 s         0     CD2
CONNECT  PTR-2  CE1 sp2       0     CD1 0     CZ  0     HE1
CONNECT  PTR-2  HE1 s         0     CE1
CONNECT  PTR-2  CE2 sp2       0     CD2 0     CZ  0     HE2
CONNECT  PTR-2  HE2 s         0     CE2
CONNECT  PTR-2  CZ  sp2       0     CE1 0     CE2 0     OH
CONNECT  PTR-2  OH  sp3       0     CZ  0     P
CONNECT  PTR-2  P   sp3       0     OH  0     O1P 0     O2P 0    O3P
CONNECT  PTR-2  O1P sp2       0     P
CONNECT  PTR-2  O2P sp2       0     P   
CONNECT  PTR-2  O3P sp2       0     P
123456789B123456789C123456789D123456789E123456789F123456789G123456789H123456789I
#-------|-----|----|----|----|----|----|---------|---------|---------|----
#        CONF  ATOM ATOM ATOM ATOM      phi0(min)  n_fold   Amplitude(barrier,kcal/mol)

DONOR    PTR01 HO2P  O2P
DONOR    PTR01 HO3P  O3P

DONOR    PTR-1 HO2P  O2P
ACCEPTOR PTR-1  O2P  P

ACCEPTOR PTR-2  O2P  P
ACCEPTOR PTR-2  O3P  P

#3.Atom Parameters: Partial Charges and Radii
# Radii from "Bondi, J.Phys.Chem., 68, 441, 1964."
RADIUS   PTR    N   1.50
RADIUS   PTR    H   1.00
RADIUS   PTR    CA  2.00
RADIUS   PTR    HA  0.00
RADIUS   PTR    C   1.70
RADIUS   PTR    O   1.40
RADIUS   PTR    CB  2.00
RADIUS   PTR   1HB  0.00
RADIUS   PTR   2HB  0.00
RADIUS   PTR    CG  1.70
RADIUS   PTR    CD1 1.70
RADIUS   PTR    HD1 1.00
RADIUS   PTR    CD2 1.70
RADIUS   PTR    HD2 1.00
RADIUS   PTR    CE1 1.70
RADIUS   PTR    HE1 1.00
RADIUS   PTR    CE2 1.70
RADIUS   PTR    HE2 1.00
RADIUS   PTR    CZ  1.70
RADIUS   PTR    OH  1.40
RADIUS   PTR    P   1.90
RADIUS   PTR    O1P 1.40
RADIUS   PTR    O2P 1.40 
RADIUS   PTR   HO2P 1.00
RADIUS   PTR    O3P 1.40
RADIUS   PTR   HO3P 1.00

CHARGE   PTRBK  N    -0.350
CHARGE   PTRBK  H     0.250
CHARGE   PTRBK  CA    0.100
CHARGE   PTRBK  C     0.550
CHARGE   PTRBK  O    -0.550
CHARGE   PTR01  CB    0.125
CHARGE   PTR01  CG   -0.125
CHARGE   PTR01  CD1  -0.125
CHARGE   PTR01  HD1   0.125
CHARGE   PTR01  CE1  -0.125
CHARGE   PTR01  HE1   0.125
CHARGE   PTR01  CZ    0.000
CHARGE   PTR01  OH   -0.360
CHARGE   PTR01  P     1.520
CHARGE   PTR01  O1P  -0.860
CHARGE   PTR01  O2P  -0.540
CHARGE   PTR01 HO2P   0.390
CHARGE   PTR01  O3P  -0.540
CHARGE   PTR01 HO3P   0.390
CHARGE   PTR01  CE2  -0.125
CHARGE   PTR01  HE2   0.125
CHARGE   PTR01  CD2  -0.125
CHARGE   PTR01  HD2   0.125
CHARGE   PTR-1  CB    0.125
CHARGE   PTR-1  CG   -0.125
CHARGE   PTR-1  CD1  -0.125
CHARGE   PTR-1  HD1   0.125
CHARGE   PTR-1  CE1  -0.125
CHARGE   PTR-1  HE1   0.125
CHARGE   PTR-1  CZ    0.000
CHARGE   PTR-1  OH   -0.360
CHARGE   PTR-1  P     1.230
CHARGE   PTR-1  O1P  -0.860
CHARGE   PTR-1  O2P  -0.540
CHARGE   PTR-1 HO2P   0.390
CHARGE   PTR-1  O3P  -0.860
CHARGE   PTR-1  CE2  -0.125
CHARGE   PTR-1  HE2   0.125
CHARGE   PTR-1  CD2  -0.125
CHARGE   PTR-1  HD2   0.125
CHARGE   PTR-2  CB    0.125
CHARGE   PTR-2  CG   -0.125
CHARGE   PTR-2  CD1  -0.125
CHARGE   PTR-2  HD1   0.125
CHARGE   PTR-2  CE1  -0.125
CHARGE   PTR-2  HE1   0.125
CHARGE   PTR-2  CZ    0.000
CHARGE   PTR-2  OH   -0.360
CHARGE   PTR-2  P     0.940
CHARGE   PTR-2  O1P  -0.860
CHARGE   PTR-2  O2P  -0.860
CHARGE   PTR-2  O3P  -0.860
CHARGE   PTR-2  CE2  -0.125
CHARGE   PTR-2  HE2   0.125
CHARGE   PTR-2  CD2  -0.125
CHARGE   PTR-2  HD2   0.125




 

